Why did Miles Davis put his finger under his ear when he stopped playing?

I would suspect that he had temporo-mandibular joint dysfunction and pain below the ear. It’s only a guess, but common to press or rub the muscles around that joint where the lower jaw (mandible) articulates with upper jaw.

I've seen him do this countless times and I believe it's either some tick, OR it's something he consciously does on purpose simply to add to the mysteriousness that of which is... Miles Davis.

Watching the Tonight Show from 1964, it seems he was angry about some aspect of the sound balance. When he does it during the blues, he changes where he's playing on the mic, putting his bell way past it, so maybe he thought he was way too hot and not balanced with the rest of the band. During So What, when he does it, he completely walks away from the mic and plays without any amplification.

The best I found via lmgtfy was these:

From reddit

I always heard Miles would cover his ears to hear the other soloist better.

OTOH, an interview side note suggests it's purely a habit:

"Had to drink some water 'cause I get dehydrated," Miles explained. "Loretta knows. Sometimes I'll say, 'Loretta, something's funny about me. What is it?' And she'll look at me and say, 'Fix your hair. It's sticking out over there.'"

Miles touches his hair behind the right ear.

"You know, Sy, chicks just know about you. Cicely [Tyson] knows when I don't feel good, and she'll call me up and say, 'What's the matter, Miles?'"

As does this review:

Every gesture seems choreographed but effortless, the way he nonchalantly walks onstage, rubs just behind his ear, puts his impeccably manicured fingers to his lips just before bringing the horn to his mouth.

I believe it was to complaint to the band of some other aspect of the performance(intonation,rhythm, etc) he did not like. I do not have any specific source to back this at the moment, though I know that he was extremely sensitive of musicians playing slightly out of tune.